RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3103
(217 letters)
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 133 bits (336), Expect = 3e-36
Identities = 43/159 (27%), Positives = 69/159 (43%), Gaps = 15/159 (9%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
+HLL E RG LE +V +MR R ++ +R + +SAT PN+ +IA WL
Sbjct: 147 IHLLDSEKRGATLEILVTKMR------RMNKALRVIGLSATAPNVTEIAEWLDADY---- 196
Query: 121 AQIDDSFRPVKLTKIVRGFPTKPSQSTFQFEMMLSYKLKSIIMQ-YSDNKPTLIFCATRK 179
+RPV L + V T F K + ++ + ++N L+F +TR+
Sbjct: 197 --YVSDWRPVPLVEGVLCEGTL-ELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRR 253
Query: 180 GVEHTCTILRQEMSIQTSPE-VREIVDKCMSNMMDNKLK 217
G E T L + E + + + + M KL
Sbjct: 254 GAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLA 292
Score = 62.5 bits (152), Expect = 1e-11
Identities = 14/54 (25%), Positives = 27/54 (50%)
Query: 8 EVREIVDKCMSNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
+ + + + M KL + +R +HHAG+ R ++E FR G + ++V
Sbjct: 274 GLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVV 327
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 127 bits (321), Expect = 4e-34
Identities = 38/146 (26%), Positives = 59/146 (40%), Gaps = 23/146 (15%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
+H L + RGPV+E+V R + +A+SATI N IA WLG
Sbjct: 154 LHYLNDPERGPVVESVTIRAKR----------RNLLALSATISNYKQIAKWLG------A 197
Query: 121 AQIDDSFRPVKLTKIVRGFPTKPSQSTFQFEMMLSYKLKS-------IIMQYSDNKPTLI 173
+ ++RPV L + V K + F+ + K+ + S N L+
Sbjct: 198 EPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQVLV 257
Query: 174 FCATRKGVEHTCTILRQEMSIQTSPE 199
F +RK E T + M+ + E
Sbjct: 258 FRNSRKMAESTALKIANYMNFVSLDE 283
Score = 62.8 bits (153), Expect = 8e-12
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 18 SNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
+ LK ++ + YHHAG+S R +IE+ FR + ++V
Sbjct: 300 GSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIV 343
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 116 bits (291), Expect = 4e-30
Identities = 40/163 (24%), Positives = 63/163 (38%), Gaps = 25/163 (15%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
+HL+G RG LE ++ M + + +SATI N ++A WL
Sbjct: 147 IHLIGSRDRGATLEVILAHML---------GKAQIIGLSATIGNPEELAEWLNA------ 191
Query: 121 AQIDDSFRPVKLTKIV--RGFPTKPSQSTFQFEMMLSYKLKSIIMQYSDNKPTLIFCATR 178
I +RPVKL + V +GF T S +F + + K LIF R
Sbjct: 192 ELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSW----EELVYDAIRKKKGALIFVNMR 247
Query: 179 KGVEHTCTILRQEMSIQTSPE----VREIVDKCMSNMMDNKLK 217
+ E L +++ + + E+ D N + KL
Sbjct: 248 RKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLA 290
Score = 64.9 bits (158), Expect = 2e-12
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 8 EVREIVDKCMSNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
+ E+ D N + KL +R + +HHAG+ ++R ++E+ FR G + +V
Sbjct: 272 ALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVV 325
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
winged-helix-turn-helix, antiparallel-coiled-COI domain,
ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
cerevisiae}
Length = 1108
Score = 45.2 bits (106), Expect = 8e-06
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 7 PEVREIVDKCMSNIMDN--------KLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLM 58
+ +I + ++ + + + +LR IG HH+G+ P + +IE LF+ G+L
Sbjct: 473 EALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLK 532
Query: 59 IL 60
+L
Sbjct: 533 VL 534
Score = 37.9 bits (87), Expect = 0.002
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
VH + ++ RG V E + +R+V +SATIPN + A W+
Sbjct: 299 VHYMRDKERGVVWEETI---------ILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPC 349
Query: 121 AQIDDSFRPVKL 132
+ +FRP L
Sbjct: 350 HIVYTNFRPTPL 361
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
2.90A {Saccharomyces cerevisiae}
Length = 1010
Score = 44.8 bits (105), Expect = 1e-05
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 7 PEVREIVDKCMSNIMDN--------KLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLM 58
+ +I + ++ + + + +LR IG HH+G+ P + +IE LF+ G+L
Sbjct: 375 EALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLK 434
Query: 59 IL 60
+L
Sbjct: 435 VL 436
Score = 37.8 bits (87), Expect = 0.002
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
VH + ++ RG V E + +R+V +SATIPN + A W+
Sbjct: 201 VHYMRDKERGVVWEETI---------ILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPC 251
Query: 121 AQIDDSFRPVKL 132
+ +FRP L
Sbjct: 252 HIVYTNFRPTPL 263
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 43.3 bits (101), Expect = 3e-05
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 8 EVREIVDKCMSNIMDN--------KLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMI 59
++ ++K ++ + K + +L I HH G+ P + +IE LF G++ +
Sbjct: 369 QIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKV 428
Query: 60 LV 61
L
Sbjct: 429 LF 430
Score = 38.3 bits (88), Expect = 0.001
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
VH + ++ RG V E V+ + Q ++F+ +SAT+PN Y+ A W+G K
Sbjct: 156 VHYVNDQDRGVVWEEVIIML---------PQHVKFILLSATVPNTYEFANWIGRTKQKNI 206
Query: 121 AQIDDSFRPVKLTK 134
I RPV L
Sbjct: 207 YVISTPKRPVPLEI 220
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 36.0 bits (82), Expect = 0.008
Identities = 34/251 (13%), Positives = 76/251 (30%), Gaps = 72/251 (28%)
Query: 1 MSIQTSPEVREIVDKCMSNIMD--NKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLM 58
+ Q P D SNI + ++ LR R + + + + L+
Sbjct: 205 LLYQIDPNWTSRSDH-SSNIKLRIHSIQAELR--------------RLLKSKPYENC-LL 248
Query: 59 ILVHLLGEESRGPVLEA--VVCR--MRTVQKSQRASQPIRFVAVSATIPNIYD------- 107
+L+++ + A + C+ + T R Q F++ + T D
Sbjct: 249 VLLNVQNAK----AWNAFNLSCKILLTT-----RFKQVTDFLSAATTTHISLDHHSMTLT 299
Query: 108 -------IALWLGFGK---PTVYAQIDDSFRPVKLTKIVRGFPTKPSQSTFQFEMMLSYK 157
+ +L P + P +L+ I + ++ + K
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTN----PRRLSIIAESIRDGLATWDN-WKHVNCDK 354
Query: 158 LKSII-MQYSDNKPTL---------IFCATRKGV---EHTCTILRQEMSIQTSPEVREIV 204
L +II + +P +F +++ ++ +V +V
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVF---PPSAHIPTILLSLIWFDVIKS---DVMVVV 408
Query: 205 DKCMSNMMDNK 215
+K + K
Sbjct: 409 NKLHKYSLVEK 419
Score = 34.8 bits (79), Expect = 0.019
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 10/55 (18%)
Query: 10 REIVDK-------CMSNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYL 57
R IVD +++ L S IG+H + +R LFR +L
Sbjct: 447 RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERM---TLFRMVFL 498
Score = 34.1 bits (77), Expect = 0.030
Identities = 27/206 (13%), Positives = 60/206 (29%), Gaps = 62/206 (30%)
Query: 45 RTIIEQLFRSGYLMILVH-LLGEESRG-PVLEAVVCRMRTVQKSQRASQPIRFVAVSATI 102
R + +L + +L+ +LG G + VC VQ +
Sbjct: 141 RQALLELRPAKN--VLIDGVLGS---GKTWVALDVCLSYKVQC--------KMDF----- 182
Query: 103 PNIYDIALWLGFGKPTVYAQIDDSFRPVK--LTKIVRGFPTKPSQST---FQFEMMLSYK 157
I+ WL + ++ L +I + ++ S+ + + +
Sbjct: 183 -KIF----WLNLKN---CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH-SIQAE 233
Query: 158 LKSIIMQYSDNKPTLIF---CATR--KGVEHTCTIL----------------RQEMSIQ- 195
L+ ++ L+ + +C IL +S+
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293
Query: 196 -----TSPEVREIVDKCMSNMMDNKL 216
T EV+ ++ K + + L
Sbjct: 294 HSMTLTPDEVKSLLLKYL-DCRPQDL 318
Score = 30.2 bits (67), Expect = 0.53
Identities = 22/178 (12%), Positives = 50/178 (28%), Gaps = 39/178 (21%)
Query: 8 EVREIVDKCMSNIMDNKLKDMLRSSIGYHH----AGMSPED-----RTIIEQ-------- 50
+V +V+K + K S+I + E+ R+I++
Sbjct: 403 DVMVVVNKLHKYSLVE--KQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460
Query: 51 ------LFRSGYLM--ILVHL--LGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSA 100
+ Y I HL + R + V R +++ R A +
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAW-NASGS 519
Query: 101 TIPNIYDIALWLGF---GKPTVYAQIDD--SFRPVKLTKIVRGFPTKPSQSTFQFEMM 153
+ + + + + P ++ F P ++ + +M
Sbjct: 520 ILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICS----KYTDLLRIALM 573
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.4 bits (75), Expect = 0.022
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 4/27 (14%)
Query: 157 KLKSIIMQYS-DNKPTLIFCATRKGVE 182
KL++ + Y+ D+ P L AT +E
Sbjct: 24 KLQASLKLYADDSAPALAIKAT---ME 47
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 33.1 bits (75), Expect = 0.061
Identities = 35/280 (12%), Positives = 70/280 (25%), Gaps = 104/280 (37%)
Query: 4 QTSPEVREIVDKCMSNIMDNKLKDMLRSSI-----------GYHHAGMSPEDRTIIEQLF 52
+TS +++ ++ DN KD SI H G + + I
Sbjct: 1637 KTSKAAQDVWNR-----ADNHFKDTYGFSILDIVINNPVNLTIHFGG--EKGKRI----- 1684
Query: 53 RSGYL-MILVHLL-GEESRGPVLEAVVCRMRTV------------QKSQRASQPIRFVAV 98
R Y MI ++ G+ + + + + Q +Q A +
Sbjct: 1685 RENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPAL-----TLM 1739
Query: 99 SATIPNIYDIALWLGFGKPTVYA-----------------QIDDSFRPVKLTKIVRG--- 138
D+ +A I+ V++ RG
Sbjct: 1740 EKAA--FEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESL---VEVVFY-RGMTM 1793
Query: 139 --FPTKPSQSTFQFEMM--------LSY---KLKSIIMQYS-----------DNKPTL-I 173
+ + M+ S+ L+ ++ + N
Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQY 1853
Query: 174 FCA-TRKGVEHTCTILR---------QEMSIQTSPE-VRE 202
A + ++ +L E+ S E V
Sbjct: 1854 VAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation,
nucleotide-binding, hydrolase, RNA-binding, ATP-binding,
DNA-binding, nuclear protein; 1.91A {Homo sapiens}
Length = 185
Score = 29.9 bits (68), Expect = 0.42
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 157 KLKSIIMQYSDNKPTLIFCATRKGVEHTCTILRQE 191
L ++ + TL+F T+KG + L E
Sbjct: 35 FLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHE 69
>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA
helicase, DEAD-BOX, ATP-binding, HE hydrolase,
mitochondrion; HET: ANP; 1.90A {Saccharomyces
cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A*
Length = 563
Score = 30.1 bits (68), Expect = 0.53
Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 3/97 (3%)
Query: 99 SATIPN-IYDIALWLGFGKPTVYAQIDDSFRPVKLTKIVRGFPTKPSQSTFQFEMMLSYK 157
SAT+ + + +A + K ++ D P +I + +
Sbjct: 271 SATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFA--NSIFAAVEH 328
Query: 158 LKSIIMQYSDNKPTLIFCATRKGVEHTCTILRQEMSI 194
+K I + N +IF T K C+IL+ E
Sbjct: 329 IKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK 365
>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase;
RECA-like fold, PRE-mRNA processing protein; 1.90A
{Homo sapiens} SCOP: c.37.1.19
Length = 172
Score = 29.5 bits (67), Expect = 0.62
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 37 HAGMSPEDRTIIEQLFRSGYLMILV 61
H GM E+R Q F+ ILV
Sbjct: 62 HRGMPQEERLSRYQQFKDFQRRILV 86
>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein,
translation; 1.75A {Saccharomyces cerevisiae} SCOP:
c.37.1.19
Length = 165
Score = 29.1 bits (66), Expect = 0.75
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 37 HAGMSPEDRTIIEQLFRSGYLMILV 61
++ + ++R I + FRSG IL+
Sbjct: 61 YSDLPQQERDTIMKEFRSGSSRILI 85
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 29.8 bits (67), Expect = 0.80
Identities = 19/98 (19%), Positives = 32/98 (32%), Gaps = 5/98 (5%)
Query: 99 SATIP-NIYDIALWLGFGKP-TVYAQIDDSFRPVKLTKIVRGFPTKPSQSTFQFEMMLSY 156
SAT+ + +A K ++ D P +I + +
Sbjct: 220 SATLDDKVQKLAN-NIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFA--NSIFAAVE 276
Query: 157 KLKSIIMQYSDNKPTLIFCATRKGVEHTCTILRQEMSI 194
+K I + N +IF T K C+IL+ E
Sbjct: 277 HIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK 314
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 29.0 bits (66), Expect = 1.1
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 4/42 (9%)
Query: 157 KLKSIIMQYSDNKPTLIFCATRKGVEHTCTILRQE----MSI 194
L ++ + TL+F T+KG + L E SI
Sbjct: 265 FLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSI 306
>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch
repair, nucleotide-binding, DNA-binding, polymorphism,
nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens}
PDB: 2wwy_A*
Length = 591
Score = 28.4 bits (64), Expect = 1.7
Identities = 7/25 (28%), Positives = 16/25 (64%)
Query: 37 HAGMSPEDRTIIEQLFRSGYLMILV 61
HA + PED+T + + + + + ++V
Sbjct: 298 HANLEPEDKTTVHRKWSANEIQVVV 322
Score = 27.6 bits (62), Expect = 3.9
Identities = 22/92 (23%), Positives = 33/92 (35%), Gaps = 13/92 (14%)
Query: 100 ATIPNIYDIALWLGFGKPTVYAQIDDSF-RPVKLTKIVRGFPTKPSQSTFQFEMMLSYKL 158
AT + D L K + SF RP L VR KPS + E ++
Sbjct: 210 ATNHVLTDAQKILCIEKCFTFTA---SFNRP-NLYYEVR---QKPSNTEDFIEDIVKL-- 260
Query: 159 KSIIMQYSDNKPTLIFCATRKGVEHTCTILRQ 190
I + +I+C ++K E L+
Sbjct: 261 ---INGRYKGQSGIIYCFSQKDSEQVTVSLQN 289
>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix,
helix-turn-helix, ATP binding, Zn(2+) binding,
hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43
c.37.1.19 c.37.1.19 PDB: 1oyy_A*
Length = 523
Score = 28.2 bits (64), Expect = 2.2
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 173 IFCATRKGVEHTCTILRQE 191
I+C +R VE T L+ +
Sbjct: 241 IYCNSRAKVEDTAARLQSK 259
>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural
genomics, structural consortium, SGC, alternative
initiation, ATP-binding, devel protein; 2.80A {Homo
sapiens}
Length = 175
Score = 27.6 bits (62), Expect = 2.3
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 37 HAGMSPEDRTIIEQLFRSGYLMILV 61
++ E R I Q FR G +L+
Sbjct: 65 SGELTVEQRASIIQRFRDGKEKVLI 89
>2jwo_A RAG-2, V(D)J recombination-activating protein 2; phosphoinositide
signaling, PHD domain, DNA recombination, DNA-binding,
endonuclease, hydrolase; NMR {Mus musculus} SCOP:
g.50.1.2 PDB: 2v83_A* 2v85_A* 2v86_A* 2v87_A* 2v88_A*
2v89_A*
Length = 82
Score = 26.2 bits (57), Expect = 3.3
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 168 NKPTLIFCATRKG--VEHTCTILRQEMSIQTSPE 199
NKP +I+C+ G V C L + I S
Sbjct: 34 NKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEG 67
>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 3.19A {Homo
sapiens}
Length = 479
Score = 27.7 bits (62), Expect = 3.6
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 37 HAGMSPEDRTIIEQLFRSGYLMILV 61
M E R + + FR G +LV
Sbjct: 364 SGEMMVEQRAAVIERFREGKEKVLV 388
>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding,
RNA binding protein; 2.10A {Saccharomyces cerevisiae}
SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A
Length = 400
Score = 27.5 bits (62), Expect = 3.7
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 37 HAGMSPEDRTIIEQLFRSGYLMILV 61
HA M ++R + FR G + LV
Sbjct: 289 HARMKQQERNKVFHEFRQGKVRTLV 313
>1yle_A Arginine N-succinyltransferase, alpha chain; structural genomics,
acyltransferase, arginine metabolism, protein structure
initiative; 1.70A {Pseudomonas aeruginosa} SCOP:
d.108.1.8
Length = 342
Score = 27.4 bits (61), Expect = 3.8
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 70 GPVLEAVVCRMRTVQKSQRAS 90
GP L A +R++ +S+
Sbjct: 259 GPTLHARTSGIRSIAQSRVVP 279
>3is6_A Putative permease protein, ABC transporter; PSI, structural
genomics, midwest center for structural genomics
structure initiative; 1.95A {Porphyromonas gingivalis}
Length = 244
Score = 27.3 bits (60), Expect = 3.8
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 114 FGKP---TVYAQIDDSFRPVKLTKIVRGFPTKPSQSTFQFEMMLSYK 157
G + S R + + + P S+ Q +M+L
Sbjct: 121 GGDVLGKRLRPAESKSDRAITIGGVFEDLP---HNSSIQADMLLPIT 164
>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase;
1.95A {Bacillus subtilis}
Length = 163
Score = 26.7 bits (60), Expect = 4.4
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 23 NKLKDMLRSSIGYH----HAGMSPEDRTIIEQLFRSGYLMILV 61
N+L D L GY H GM EDR + F+ G LV
Sbjct: 49 NQLTDELDDL-GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLV 90
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 27.1 bits (61), Expect = 4.5
Identities = 7/25 (28%), Positives = 9/25 (36%)
Query: 37 HAGMSPEDRTIIEQLFRSGYLMILV 61
+ R I FR G +LV
Sbjct: 388 TGNLEGAQRDAIMDSFRVGTSKVLV 412
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 27.1 bits (59), Expect = 4.9
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 8 EVREIVDKCMSNIMDNKLK--DMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
RE K ++ ++ + +K + + + G+S ++ +I F G +LV
Sbjct: 369 NYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLV 424
>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene
regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19
c.37.1.19 PDB: 1xtj_A* 1xtk_A
Length = 391
Score = 26.8 bits (60), Expect = 6.0
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 37 HAGMSPEDRTIIEQLFRSGYLMILV 61
H GM E+R Q F+ ILV
Sbjct: 281 HRGMPQEERLSRYQQFKDFQRRILV 305
>1t8t_A Heparan sulfate D-glucosaminyl 3-O- sulfotransferase 3A1;
alpha-beta motif, substrate-binding cleft; HET: A3P CIT;
1.85A {Homo sapiens} SCOP: c.37.1.5 PDB: 1t8u_A*
Length = 271
Score = 26.7 bits (58), Expect = 6.2
Identities = 7/52 (13%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 16 CMSNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILVHLLGEE 67
C+ + L + G H + E + + +R + + + G +
Sbjct: 216 CLKKAEGSSRPHCLGKTKGRTHPEIDREVVRRLREFYRP-FNLKFYQMTGHD 266
>3mos_A Transketolase, TK; thiamin diphosphate TPP THDP enzyme catalysis
sugar metaboli transferase; HET: TPP; 1.75A {Homo
sapiens} PDB: 3ooy_A*
Length = 616
Score = 26.7 bits (60), Expect = 7.3
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 168 NKPTLIFCATRKG 180
++PT I T KG
Sbjct: 231 HQPTAIIAKTFKG 243
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 26.1 bits (58), Expect = 7.9
Identities = 7/35 (20%), Positives = 12/35 (34%), Gaps = 2/35 (5%)
Query: 157 KLKSIIMQYSDNKPTLIFCATRKGVEHTCTILRQE 191
L + + P LIF + V+ L +
Sbjct: 45 YLLECLQKTPP--PVLIFAEKKADVDAIHEYLLLK 77
>2z6g_A B-catenin; FULL-length, beta-catenin, cell adhesion; 3.40A {Danio
rerio}
Length = 780
Score = 26.1 bits (57), Expect = 9.9
Identities = 11/54 (20%), Positives = 21/54 (38%)
Query: 41 SPEDRTIIEQLFRSGYLMILVHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIR 94
+ + L ++V LL S P+++A V +R + P+R
Sbjct: 474 HQDAEMAQNAVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLALCPANHAPLR 527
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.134 0.388
Gapped
Lambda K H
0.267 0.0478 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,195,304
Number of extensions: 180320
Number of successful extensions: 480
Number of sequences better than 10.0: 1
Number of HSP's gapped: 466
Number of HSP's successfully gapped: 53
Length of query: 217
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 127
Effective length of database: 4,188,903
Effective search space: 531990681
Effective search space used: 531990681
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.6 bits)